Collaborative github in Rstudio


MozFest2016, London, Sat 29 Oct. 1:00 - 3:00 pm

Open Science, Floor 9 - 903

Anna Krystalli @annakrystalli | Sharada Prasanna Mohanty @MeMohanty


handout: https://annakrystalli.github.io/Mozfest_github-rstudio/index.html


Session Roadmap


1 Introductions

- get to know the audience (10 mis)

  • Shout outs and twitter polls.

- get to know github (25 mins)

  • github as a computational research tool


2 Get stuck in

- Version control with github and rstudio (40 mins)

  • In this session, we are going to get you started with using version control from within RStudio.

  • The material is self-paced and includes a worked-example. It is suggested that you work through the sections in order.

- Collaborative github through rstudio #EvoLottery (40 mins)

  • In this exercise, each participant will fork a github repo, and contribute a file required to simulate the evolutionary trajectory of an imaginary species’ body size.

  • We’ll use github to collate all species files and plot them all up together at the end! We’ll also discover the skull and beak shapes associated with each simulated species size.



introductions: get to know the audience

Check #EvoLottery tweets for live twitter polls!


introductions: get to know github


version control and computing

"The need for a logical way to organize and control revisions has existed for almost as long as writing has existed, but revision control became much more important, and complicated, when the era of computing began."


version control and science

  • long been used to maintain code repositories in the software industry

    especially in open source software

  • science increasingly computational

    demands for increased openness and transparency


http://billmills.github.io/scienceXpython/


modern science workflows

can be overwhelming


succesful modern science workflows

can be extremely powerful



github for science

ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts.

more on github for science


Github as part of Good Enough Practices in Scientific Computing

e.g My research workflow, based on Github by Carl Boettiger


Rstudio for r users


invest in next generation science skills


  • …and super-charge your teams!

  • …or get left behind



why github?

empowers collaboration

repos

centralising information e.g. ROpenSci / rfishbase


issues

project management


commits

project tracking



fosters reproducibility

commits

traceability



entire process of project evolution reproducible



PRACTICALS


Practical 1: Github & Rstudio for version control

Code Cafe Style tutorial by Mike Croucher that will get you set up with all required software and able to link rstudio projects to github repos.

Enter Practical




Practical 2: Github & Rstudio for collaborative coding

#EvoLottery

Beak and skull shapes in birds of prey (“raptors”) are strongly coupled and largely controlled by size.

  • In this exercise, each participant will fork a github repo, and contribute a file required to simulate the evolutionary trajectory of an imaginary species’ body size.

  • We’ll use github to collate all species files and plot them all up together at the end! We’ll also discover the skull and beak shapes associated with each simulated species size.

Enter Practical